ORIGINALPAPER A. El Amrani ® L. Marie ® A. Aı¨nouche ® J. Nicolas I. Coue´e Genome-wide distribution and potential regulatory functions of AtATE, a novel family of miniature inverted-repeat transposable elements in Arabidopsis thaliana Received:25November2001/Accepted:5April2002/Publishedonline:15May2002 Ó Springer-Verlag 2002 Abstract A study of transgenic promoter::b-glucuroni- dase lines showed that the promoters of the two Ara- bidopsis ARGININE DECARBOXYLASE paralogues, ADC1 and ADC2,exhibitedextremelydifferentpatterns ofactivity.Onemajorfeatureofthepromoterof ADC1 wasthepresenceofanoveltransposableelement,which wasshowntopossessallofthecharacteristicsofMin- iatureInverted-repeatTransposableElements(MITEs), and to be present in 26 full-length copies and 1617 partialcopiesandfragmentsdistributedthroughoutthe Arabidopsisgenome.TRANSFACanalysisshowedthat thistransposableelementpossessesasignificantnumber oftranscription-factorbindingmotifs.Abioinformatics approachbasedonasuffix-treecompilationwasusedto obtainanexhaustivedescriptionofexactcopynumbers andpositionsoftheelementintheArabidopsisgenome. The distribution among the chromosomes was non- random,andasignificantnumberofcopieswerefound in regions flanking genes. Full-length copies of the transposable element were detected in the immediate vicinityof22genes,eitherupstreamordownstream. Keywords MITEs(MiniatureInverted-repeat TransposableElements) ® Argininedecarboxylase ® Bioinformatics ® Genomesequence ® Arabidopsis Introduction Two major classes of mobile genetic elements are clas- sicallyconsidered.ClassIelements,orretrotransposons, transpose through reverse transcription of an RNA in- termediate (Kumar and Bennetzen 1999). LTR retro- transposons are characterised by the presence of long terminal repeats. Non-LTR retrotransposons, such as LINEs (long interspersed repetitive elements) and SINEs(shortinterspersedrepetitiveelements),lackthese characteristic sequences (Kumar and Bennetzen 1999). ClassIIelementstransposeviaaDNAintermediateand are characterised by the presence of terminal inverted repeats(TIRs)(Casacubertaetal.1998;Leetal.2000). Some elements are difficult to classify (Feschotte and Mouche`s2000a).SuchisthecaseforMiniatureInvert- ed-repeat Transposable Elements (MITEs), which were firstdescribedinplants(Wessleretal.1995)andlaterin otherorganisms(Tu1997). Arabidopsis thaliana has one of the smallest known genomes among higher plants (The Arabidopsis GenomeInitiative2000).Allofthepreviouslydescribed classes of mobile genetic elements, including MITEs, havebeenfoundinitsgenome(Casacubertaetal.1998; KumarandBennetzen1999;Leetal.2000),andcom- plete genome sequence information has been available sincetheendof2000(TheArabidopsisGenomeInitia- tive2000).Thissequenceisthereforeapowerfulmodel forgenome-wideanalysisofthevarietyanddistribution of transposable elements and their potential impact on geneexpression. Inthepresentstudy,thesequestionswereapproached asaresultofanalysingthetranscriptionalregulationof ARGININE DECARBOXYLASE (ADC)genesinAra- bidopsisatthepromoterlevel.Theenzyme(EC4.1.1.19) encodedbythesegenescatalysestheformationofagm- atine from L-Arg, which is the committed step at the initiation of polyamine synthesis. Polyamines are ubiq- uitousgrowthregulatorsinprokaryoticandeukaryotic organisms, and have been implicated in a range of MolGenetGenomics(2002)267:459–471 DOI10.1007/s00438-002-0675-4 CommunicatedbyG.P.Georgiev A.ElAmrani(&) ® L.Marie ® A.Aı¨nouche ® I.Coue´e CentreNationaldelaRechercheScientifique, Universite´ deRennes1,UMR6553, CampusdeBeaulieu,Baˆtiment14, 263AvenueduGe´ne´ralLeclerc, 35042RennesCedex,France E-mail: Abdelhak.Elamrani@univ-rennes1.fr Fax:+33-2-23235026 L.Marie ® J.Nicolas InstitutdeRechercheenInformatique etSyste`mesAle´atoires,Universite´ deRennes1, CampusdeBeaulieu,Baˆtiment12A, 263AvenueduGe´ne´ralLeclerc, 35042RennesCedex,France